If you replaced the pads, and still have a bad pedal,
I would second the guess that your rears need adjusted.

I know that mine do.  If you have a pair of very large
channel locks, pushing the piston back into the caliper
shouldn't be very hard.  Just clamp on and squeeze.  
Use the old pad to protect the piston from damage.

Also make sure that the mounting pins and all other sliding
points are rust free/clean and to put anti seize on them so
that everything keeps moving as needed.  This will help
the pads to wear a bit more evenly.  If the caliper can't float
for some reason, you usually end up with one pad worn to the metal,
and other looking brand new.

Permatex and others make disc brake anti squeal goo to put on
the back of the pads.  We usually coat the pads with this on the
back to (you guessed it) prevent squealing.  Also, there may be
tabs that need to bent over to keep the pads from rattling.
I honestly don't know if VW has these.

It has been recommended to replace all of the brake fluid when doing
a brake job.  I don't do it, but them I'm lazy, and likely won't sue myself
for my own negligence.  Its to keep water and contaminents from accumulating
in proportioning valves and the calipers where they can greatly accellerate wear.
 
I would do the 2 year replacement thing, though.

 
Did later years of Vanagons have self adjusters?
If so, I wonder if these could be retrofitted to say,
something like my '77?

Matt